sideViolin {scDD} | R Documentation

## sideViolin

### Description

Plots two histograms side by side with smoothed density overlay

### Usage

    sideViolin(y, cond, MAP = NULL, logT = TRUE, title.gene = "",
      conditionLabels = unique(cond), axes.titles = TRUE)

### Arguments

`y` | Numeric vector of data to plot.
`cond` | Vector of condition labels corresponding to elements of `x`.
`MAP` | List of MAP partition estimates with conditions as list items and samples as elements (integer indicating which cluster each observation belongs to; zeroes belong to cluster 1)
`logT` | Logical that indicates whether to take the log(x+1) transformation.
`title.gene` | Character vector that contains the gene name that you are plotting.
`conditionLabels` | Character vector containing the names of the two conditions.
`axes.titles` | Logical indicating whether or not to include axes labels on plots.

### Value

ggplot object

### References

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y

### Examples

    # load toy simulated example ExpressionSet to find DD genes

    data(scDatExSim)

    # load SingleCellExperiment package to facilitate subset operations

    library(SingleCellExperiment)

    # plot side by side violin plots for Gene 1 (DE)

    sideViolin(normcounts(scDatExSim)[1,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[1])

    # plot side by side violin plots for Gene 6 (DP)

    sideViolin(normcounts(scDatExSim)[6,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[6])

    # plot side by side violin plots for Gene 11 (DM)

    sideViolin(normcounts(scDatExSim)[11,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[11])

    # plot side by side violin plots for Gene 16 (DB)

    sideViolin(normcounts(scDatExSim)[16,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[16])

    # plot side by side violin plots for Gene 21 (EP)

    sideViolin(normcounts(scDatExSim)[21,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[21])

    # plot side by side violin plots for Gene 26 (EE)

    sideViolin(normcounts(scDatExSim)[26,], scDatExSim$condition,
               title.gene=rownames(scDatExSim)[26])

[Package scDD version 1.8.0 Index]